Dearest 'dreamer'... may you have peace!
The 'water' never 'went' anywhere.
Exodus 30:17-21
Revelation 4:6
Revelation 22:1
Just as it is contained in the physical realm as H20, it is also contained in the spiritual one... as holy spirit... the 'water of life', 'life's water'... and 'the bath that cleanses'. That is why the priests had to bathe in the copper basin, to symbolize being CLEANSED, in the manner that we must be 'bathed' in holy spirit to be 'cleansed'.
What took place on the second day, however, was not labeled 'good', as the water was not 'created', as were "Light", the "Earth", the "heavens", "the luminaries", "vegetation", etc. Only that which was created was deemed 'good'. The water, HOLY SPIRIT, however, along with JAH and 'Darkness'... already existed. None of the three were 'created'.
Thus, 'God saw everything that He had MADE... and look! it was good'.
Genesis 1:31
I hope this helps, and bid you peace!
A slave of Christ,
SJ